[AMBER] ligand molecule problem

From: tianchuan881 <tianchuan881.hotmail.com>
Date: Mon, 11 Mar 2013 11:08:09 +0800

Dear amber,
In my simulation process, the ligand molecule has broken into parts when I save new pdb files by the end of tleap. I re-checked my preparation process as follows. I hope you could help me solve this problem. The new pdb file and ligand files has been attached.

best regards,
tianchuan


Welcome to LEaP!
(no leaprc in search path)
Sourcing: /software/amber11/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /software/amber11/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /software/amber11/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /software/amber11/dat/leap/lib/all_nucleic94.lib
Loading library: /software/amber11/dat/leap/lib/all_amino94.lib
Loading library: /software/amber11/dat/leap/lib/all_aminoct94.lib
Loading library: /software/amber11/dat/leap/lib/all_aminont94.lib
Loading library: /software/amber11/dat/leap/lib/ions94.lib
Loading library: /software/amber11/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /software/amber11/dat/leap/cmd/leaprc.gaff
----- Source of /software/amber11/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /software/amber11/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end
> R = loadmol2 R.mol2
Loading Mol2 file: ./R.mol2
Reading MOLECULE named R
> check R
Checking 'R'....
Checking parameters for unit 'R'.
Checking for bond parameters.
Could not find bond parameter for: sx - cd
Checking for angle parameters.
Could not find angle parameter: sx - cd - na
Could not find angle parameter: sx - cd - nc
Could not find angle parameter: o - sx - cd
Could not find angle parameter: c3 - sx - cd
There are missing parameters.
Unit is OK.
> loadamberparams R.frcmod
Loading parameters: ./R.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveoff R R.lib
 Creating R.lib
Building topology.
Building atom parameters.
> saveamberparm R R.prmtop R.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 13 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        R 1
  )
 (no restraints)
> loadoff R.lib
Loading library: ./R.lib
>




tianchuan881

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Received on Sun Mar 10 2013 - 20:30:03 PDT
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